loadViralPop: loadViralPop

In SMITIDstruct: Data Structure and Manipulations Tool for Host and Viral Population

Description

Load all ViralPop observated in the file.obs

Usage

loadViralPop(directory, listFiles, listCol = list(id = "id", timeObs =
  "time", filename = "filename"), file.extension = "fasta")

Arguments

directory	path where is data
listFiles	a dataframe with host ID, time observation and file name (filename.fasta)
listCol	a list of listFiles colomns names ("id", "timeObs", "filename")
file.extension	genotype file extension

Value

a vector of VirlaPop object

Examples

path = system.file("extdata", "data-simul/", package="SMITIDstruct")
files <- list.files(path, pattern = ".*.fasta" ,full.names=FALSE)
lfileinfo <- sapply(files,function(x){return(substr(x,1,nchar(x)-6))})
splitFiles <- strsplit(lfileinfo, "_");
listF <- cbind(data.frame(matrix(unlist(splitFiles),nrow=length(splitFiles), byrow=TRUE),
               stringsAsFactors = FALSE), names(splitFiles))
colnames(listF) <- c("id", "time", "filename")
lvpop <- loadViralPop(path,listF)

SMITIDstruct documentation built on June 14, 2019, 5:04 p.m.